[R] SOM code + visualization aspects

[John Aitchison]

On 1 Mar 2001, at 7:11, niels Waller wrote:

> 
> The (slow) SOM code can be found on my web page (towards the bottom)
> 
> http://peabody.vanderbilt.edu/depts/psych_and_hd/faculty/wallern/

Thank you, I have tested it (well, on toy examples) and it works just fine 
- as a clustering tool. How 'slow' it is I don't know - as in, I have not 
tested it on large problems - but in any event the Kaski* paper (below) 
suggests some possible speedups.

SOM, I think, is a bit of a moving target, but as well as the clustering 
aspect there appears to be also a data visualisation aspect which is not 
represented in your code as far as I could see.  Paraphrasing Kaski, one 
implements a regular 2d grid on which 'units' are located  : each unit has 
a 'reference vector' (a vector of means), the 'winning unit'  for a given 
input vector (based on Euclidean distance in the 'measurement space') has 
its reference vector updated as do its neighbours in 'grid space' (with 
weights approc proportional to 1/distance in the GRID SPACE) . Eventually 
this process organizes the data on the grid in some meaningful fashion.  
You can then use this grid as an 'ordered groundwork' on which you can 
display a bunch of things .. the original measurement variables, cluster 
densities etc.  It has a certain appeal imho.

 
 * Samuel Kaski's thesis "Data exploration using self-organizing 
maps"  is at http://www.cis.hut.fi/~sami/thesis.ps

 

John Aitchison
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